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Soybean Biotechnology: An Outlook

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The article provides a bird eye view on soybean biotechnology and molecular biology research and achievements world over. The hugely successful genetic modifications of soybean coupled with genome sequecing project by Department of energy-Joint genome initiative (DOE-JGI) with potential implications for biofuel exploitation of the crop makes it one of the most loved species by ..

•Soybean diploid chromosome number of the organism: 40
(Haploid chromosome in the gametes/ sex cells 20)

•Soybean genome sequence project: Version 1 of the genomic sequence of the soybean cultivar William 82 (Wm 82) has been completed by Community sequencing Program (CSP) by a consortium led by Gary Stacey, Randy Shoemaker, Scott Jackson, Jeremy Schmutz, and Dan Rokhsar.
•A preliminary assembly and annotation of the soybean genome,has been made available by the U.S. Department of Energy Joint Genome Institute (DOE JGI), to the greater scientific community with the greater emphasis on bio-energy research.
"Glyma 0": The preliminary data set on soybean genome is called as glyma0
"Glyma 1": The first chromosome-scale assembly of the soybean genome is called as "Glyma1"
•Size of the genome: approximately 1,112 MB;
•Protein coding loci (No of genes) predicted ~66153
•EST (Expressed Sequence Tags) genes: 32317 genes
•About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination.
•Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies.
•Phaseoloid Genomics :Phaseolus vulgaris (bean) earns primary interest as a diploid model species for syntenic genome sequence comparisons with soybean. Phaseolus has much in common with Glycine (e.g., determinate nodules), and may be very useful for discovery of genes involved in abiotic stresses (e.g., phosphorus, drought)
•Legume genomics: Implementation of a coordinated effort for research & evelopment of genomics across the legume family facilitated progress in the model species Medicago truncatula and Lotus japonicus and in soybean (Glycine max); and accentuated the need to transfer genomic information from the model species to cool-season pulses
•The perennial species, constituting the secondary germplasm pool for soybean, represent an untapped resource for a wide range of agronomically important traits such as drought tolerance and rust resistance. Some of these have been studied (e.g., rust resistance in G. canescens, G. tomentella).
•Related genera: Besides the perennial species of Glycine, genomes of other genera are important since they can fill the temporal gap between Phaseolus and Glycine.
o Teramanus: one of the closest generic relatives of Glycine, have relatively large genomes and are not of economic interest.
o Pachyrhizus (jicama) is of economic importance in the developing world.
o Pueraria lobata (kudzu) is a weed that is closer to Glycine
•Transposons - known as McClintocks's 'jumping genes' - are ubiquitous in plant genomes and confound the assembly and annotation of the genomes. Researchers at Purdue University identified 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear insertion sites. These elements, together with numerous truncated elements/fragments, make up approximately 61% of the soybean genome.
• SNARE: Soybean Nonautonomous and Autonomous Retrotransposon Element (SNARE)

Molecular markers for soybean improvement:• RFLP (Restriction Fragment Length Polymorphism): In 1990, the first RFLP-based map of the soybean genome was published (Keim, Diers, Olson, & Shoemaker,1990).
• SSR (Simple Sequence Repeats): The development and mapping of a large set of soybean simple sequence repeat (SSR) markers were initiated in 1995
• Molecular marker development in soybean has progressed from RFLPs to SSRs and now to single nucleotide polymorphisms (SNPs)
Soybean transformation: •Although the production of fertile transgenic soybean plants was first achieved with a particle bombardment (biolistic) method and Agrobacterium-mediated transformation almost 2 decades ago and transformation protocols have since improved and become more efficient soybean has remained recalcitrant to routine transformation.
•Explants used for regeneration: Cotyledons, cotyledonary nodes, apical meristem, embryogenic callus, embryo axes.
•Preferred Methods of transformation: Agrobacterium mediated and Particle bombardment
•Current transformation efficiencies are approximately 3.5% using the organogenesis approach and approximately 25% using transformation of somatic embryos.
•Somatic embryogenesis in soybean was first achieved by Christianson et al. (1983). In this process, adventive somatic embryos are induced from immature cotyledons cultured on medium containing moderately high concentrations of auxin, either 2,4-dichlorophenoxyacetic acid (2,4-D) or ®-naphthaleneacetic acid, and are used to generate proliferative embryogenic cultures and to recover whole plants through maturation and germination. The formation of proliferative embryogenic tissue is dependent on genotype, and the application of transformation has thus been limited to a few soybean varieties (cv Jack)

Web based resources:
•SoyTE, the soybean transposable element database
•SoyBase: It is a web-based resource that displays integrated views of the genetic, physical and sequence maps of soybean.
•Soybean genome data: The genome sequence data can be accessed at phytozome site

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